Semi-Quantitative Group Testing: A Unifying Framework for Group Testing with Applications in Genotyping

Abstract

We propose a novel group testing method, termed semi-quantitative group testing, motivated by a class of problems arising in genome screening experiments. Semi-quantitative group testing (SQGT) is a (possibly) non-binary pooling scheme that may be viewed as a concatenation of an adder channel and an integer-valued quantizer. In its full generality, SQGT may be viewed as a unifying framework for group testing, in the sense that most group testing models are special instances of SQGT. For the new testing scheme, we define the notion of SQ-disjunct and SQ-separable codes, representing generalizations of classical disjunct and separable codes. We describe several combinatorial and probabilistic constructions for such codes. While for most of these constructions we assume that the number of defectives is much smaller than total number of test subjects, we also consider the case in which there is no restriction on the number of defectives and they may be as large as the total number of subjects. For the codes constructed in this paper, we describe a number of efficient decoding algorithms. In addition, we describe a belief propagation decoder for sparse SQGT codes for which no other efficient decoder is currently known. Finally, we define the notion of capacity of SQGT and evaluate it for some special choices of parameters using information theoretic methods.